2KWJ: Histone peptide

Solution structures of the double PHD fingers of human transcriptional protein DPF3 bound to a histone peptide containing acetylation at lysine 14. Determined by solution NMR. Released 14 Jul 2010.

Method: Solution NMR
Organism: Homo sapiens
Chains: 2
Atoms: 1,040
Mol. weight: 15.24 kDa
Ligands: ZN
Released: 14 Jul 2010

Explore 2KWJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2KWJ contains 3 α-helices and 7 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	268	1	2
β-strand	271	1	2
β-strand	282-283	2	3
β-strand	290-291	2	3
α-helix	300-308	9
α-helix	314-316	3
β-strand	331-333	3	1
β-strand	340-342	3	1
α-helix	361-369	9

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone peptide	B	protein	20		P68431 (AlphaFold model)
Zinc finger protein DPF3	A	protein	114	Homo sapiens	Q92784 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>2KWJ_1 Histone peptide (chains B)
ARTKQTARKSTGGKAPRKQL

Sequence of entity 2 (A), FASTA

>2KWJ_2 Zinc finger protein DPF3 (chains A)
GSYCDFCLGGSNMNKKSGRPEELVSCADCGRSGHPTCLQFTLNMTEAVKTYKWQCIECKS
CILCGTSENDDQLLFCDDCDRGYHMYCLNPPVAEPPEGSWSCHLCWELLKEKAS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b. Zeng, L., Zhang, Q., Li, S. et al. Nature (2010) 466:258-262. DOI 10.1038/nature09139 · PubMed

Other PDB entries of the same protein (UniProt P68431 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5SVY 1.05 Å, MORC3 CW in complex with histone H3K4me1
2V89 1.1 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
5SZC 1.19 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
4UP0 1.28 Å, Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and…
5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
4L7X 1.35 Å, Crystal structure of the DIDO PHD finger in complex with H3K4me3
6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail

Browse structure collections

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